Friday, September 30, 2011

What can evolution tell us about domestic violence? Two researchers in the US suggest such violence has ancient origins and that establishing evolution's role could help to better identify those at risk. Others argue that the research makes simplistic assumptions, and warn that some people will interpret the research as an excuse for violence.

Each year more than 500,000 women in the US alone report to the police violent attacks by current or former male partners. There is a reason why domestic violence is so widespread, says David Buss, an evolutionary biologist at the University of Texas in Austin: it carries a selective advantage, tied with reproductive success. In other words, men who are violent are trying to make sure that their partner has his child and not another man's.

Let's think about this for a minute.

In order for violence against women to have a selective advantage there has to be an important genetic component. Let's imagine a time back in hunter-gather days when there were two groups of men who differed in their violence-against-women alleles. One group was kind and considerate toward their female companions. They treated them with respect. The other group treated women as property and often beat them in order to prevent imagined infidelity. Somehow the violent group managed to mate more frequently and/or have more children than the kind group so the allele for kindness and respect was eliminated from the population.

Lots of things had to happen in order for this scenario to play out as the evolutionary psychologists imagine. For example, women had to prefer to have children with men who would beat them. (Or maybe they were forced to mate with the violent men.). Furthermore, there had to be no consequences for the men who beat their mates. The other members of the group had to tolerate that behavior even if they found it repulsive.

If the scenario is correct then most men—including you and I—have to carry the violence-against-women allele since it was selected in the past. This seems very strange since most men don't beat their wives.1 I guess we have learned to suppress the genetic urge. But why would we do that if it's a selective advantage to engage in domestic violence?

There's also something seriously wrong with men who engage in domestic violence. They are assholes who deserve very little sympathy from the rest of society. I suspect they got no sympathy in ancient hunter-gather societies either. There is no gene that makes you act like an asshole. That's all due to nurture and it can be changed if we put our minds to it.

1. At least I think this is true. When was the last time you beat your wife or girlfriend?

We discussed Young Earth Creationism in our last class. As most of you know, the Young Earth Creationist believes that the universe was created about 10,000 years ago and that all modern species (or kinds) were created simultaneously at that time. This view is compatible with the Genesis story in the Bible.

How is it possible for someone in the 21st century to ignore all the scientific evidence supporting an Earth that has been around for 4.5 billions years and an universe that is even older? We tried to come up with the most common ways that Young Earth Creationists can rationalize the obvious conflict.

The most obvious explanation is that they are completely unaware of the massive amount of scientific evidence that conflicts with their belief. In other words, they simply don't see a conflict between science and their religion because they have never been taught proper science. I suspect this is true of the vast majority of Young Earth Creationists.

But there's a subset of them who know the science. They have to come up with some sort of explanation that makes their position compatible with the findings of science. We identified two sorts of explanation that seem to apply.

1. Reject the scientific evidence as unreliable and try to discredit scientists. This path gives rise to talking points about the errors in carbon-14 dating and the fact that atheist scientists are blinded by their "religion."

2. Rely on faith and revelation as superior paths to knowledge. This means that the scientific "evidence" must be wrong even though the flaws aren't obvious. It must be wrong because it conflicts with God's word and there's no more reliable indicator of truth than the word of God.

(Sometimes the superiority of faith leads to the conclusion that God must have deliberately created an Earth with the illusion of age. It's not clear why God did this but we are not in a position to question God's wisdom in this matter.)

The BioLogos Foundation has, until recently, promoted theistic evolution. This worldview tends to accept scientific evidence as much as possible. Theistic Evolutionists, for example, are perfectly happy with a 4.5 billion year old Earth.

There are many things that are harmful to children—poverty and war come to mind. There's also superstition and ignorance.

Believe it or not, there are many parents who think that electromagnetic radiation from WiFi transmitters is harming their children. They want it removed from schools because their children are becoming sick when they are at school.

Steve Thoms at Skeptic North has a post on this issue [Why, Wifi? Why?]. He explains why some people believe stupid things and how they go about defending those beliefs in a scientific society. He also raises questions about the "evidence" of illness caused by WiFi.

Creationism and "intelligent design" are not scientific theories, but they are portrayed as scientific theories by some religious fundamentalists who attempt to have their views promoted in publicly-funded schools. There should be enforceable statutory guidance that they may not be presented as scientific theories in any publicly-funded school of whatever type.

But this is not enough. An understanding of evolution is central to understanding all aspects of biology. The teaching of evolution should be included at both primary and secondary levels in the National Curriculum and in all schools.

Nobody can argue with the second part of the statement; of course evolution should be taught.

I want to challenge the first part of the statement. Should the British government pass a law banning the teaching of creationism and/or Intelligent Design Creationism as science?

The first thing that troubles me is the idea of a legal ban on teaching anything at all. I don't think this is a good idea even for ridiculous ideas such as homeopathy or astrology. Do we really want lawyers and legislators making decisions about what should be taught as science and what shouldn't? Neither of those groups are competent to make such decisions.

Besides, enforcing a legal prohibition against teaching Intelligent Design Creationism as science only plays into the hands of the creationists. What are we afraid of? Are we worried that the creationist challenge is so strong that science may not be able to withstand the assault without protection from the courts?

There's another issue that's even more troubling. We could read between the lines of the joint statement and come up with the following logic ...

We the undersigned have adopted a particular version of what science is and we have adopted a particular definition of intelligent design. We agree on a particular (unstated) definition of "scientific theory." According to these views and definitions, intelligent design is not science and should not be taught as science in our schools.

Problem is, there are many different definitions of science and why should we believe this group of signatories over another? There are also many different ways of defining intelligent design and some of the definitions fit my view of what science is. It may be horrible science but it can't just be dismissed as non-science.

On this blog we often discuss books by Intelligent Design Creationists. Most of what's in The Myth of Junk DNA or The Edge of Evolution, for example, is pure science by any definition. It turns out to be bad science—or a very misleading version of science—but on the surface it seems to apply rational thought, evidence, and skepticism to the problem of evolution.

I'm very uncomfortable with the idea that those books should be banned from science classes.

There's another reason why banning bad science is wrong. Study after study has shown that in order to correct student misconceptions you need to address those misconceptions directly. For example, if a student comes into a classroom thinking that creationism is correct, they will not be swayed by simply presenting the evidence for evolution. That's necessary but not sufficient. You also have to show them why their creationist views are wrong and that means bringing up those incorrect views in science class.

Take irreducible complexity as an example. If students think that irreducible complexity refutes evolution then you aren't ever going to change their minds by ignoring irreducible complexity in class. What you have to do is explain the concept and demonstrate why it's bad science (or non-science if you prefer). You can't do this if you are legally prohibited from mentioning intelligent design in a science class.

We need to teach students what science is and what science isn't. The appropriate place to do this is in science class. You can't teach this concept without giving some examples of non-science or pseudoscience and that's a good thing because it directly addresses any misconceptions students might have.

Similarly, if Intelligent Design Creationism is mostly bad science (instead of non-science) then the best way to teach the difference between good science and bad science is to use examples and Intelligent Design Creationism is an excellent example because so many students think it's good science. Banning it from the science classroom is just bad pedagogy.

It's also counter-productive. By protecting it from direct critical analysis in a science class you are actually giving a free pass to the anti-science forces outside the classroom.

Monday, September 26, 2011

A blog started by two graduate students, 11000 kilometres apart, on a quest to discover, or otherwise invent, the holy grail of bioengineering: rational protein design.

Our blog consists of weekly reviews of important papers within the cutting edge field that is an amalgam of theoretical and experimental biology, fused with a heavy dose of computational engineering. At the same time, our posts are accessible to even the keen undergraduate in science or engineering.

In nature, new proteins are created by means of mutations and recombination in the DNA, a process that can take thousands of years, and only then, whose purpose serves only strengthen the fitness of the host organism, a purpose often ill-suited for industry or medicine. Protein engineering aspires to create new proteins within a year or less, using powerful computational and experimental techniques such as simulation and directed evolution to create custom-tailored proteins designed especially for industry or medicine.

But more importantly, we hope to fascinate our readers with the immense possibilities of protein engineering. So that perhaps one day, you too, will become a proteneer.

Thursday, September 22, 2011

Most civilized, democratic countries have abolished capital punishment. This is especially true of those countries with a Christian tradition.

The last execution in Canada took place in 1962 and the last one in Mexico was in 1961. Here's a short list of other countries with the last year of execution: Australia (1967), Israel (1962), Brazil (1876), Argentina (1916), United Kingdom (1964), France (1977), and Italy (1947).

[Blue: capital punishment abolished for all crimes; Green: abolished for all crimes expect some committed in exceptional circumstances; Brown: abolished in practice; Red: legal form of punishment]

The United States differs from its geographical and cultural neighbors. Why does the United States still carry out executions in 2011 when the practice has ceased in all those countries with a similar cultural and religious background?

Saturday, September 17, 2011

In my class on Scientific Misconceptions and Controversies we discuss the ways in which scientific reasoning is used and misused in debates and discussions.

As a general rule, you can divide scientific debates into two main categories: (1) genuine scientific controversy that hasn't been resolved, or (2) misconceptions or misunderstandings of the science by one or more of the sides. The third category is genuine fraud.

Sometimes it's really hard to decide when a misconception turns into lying (fraud). This is particularly true in the evolution/creation debate where some of the most outlandish claims by the creationists have been refuted again and again but continue to be used. Are those creationists so stupid that they just don't understand why they are wrong or is it more likely that they know they are wrong but are just taking advantage of the ignorance of their audience to promote a good-sounding talking point?

In August we noted that National Center for Science Education was running a bumper sticker contest

They may have declared their winner. Folk have been seeing this bumper sticker around town:

We have the fossils. We win.

That would be good news for Darwin, who didn’t think the fossil record supported him, but hoped it would, one day.

The trouble is, that has been the trade secret of paleontology (Stephen Jay Gould) that it doesn’t support him. It supports sudden, rapid emergence, which almost certainly means a non-Darwinian origin for change in life forms.

The issue is whether the fossil record, taken as a whole, supports the transformation of one type of organism into another. The answer is overwhelmingly "yes." There are dozens of excellent examples including our own species.

These examples have been described in detail in an attempt to educate the creationists but all this to no avail. They continue to repeat the myth that the fossil record does not support evolution in spite of the enormous efforts made by evolution supporters to correct their ignorance.

At some point we need to stop attributing this behavior to mere stupidity and ignorance and start recognizing it for what it is—a lie. Denyse knows the truth but continues to repeat a false claim.

You know the article is going to be misleading as soon as you read the opening paragraph.

When the first draft of the human genome finally became available, there were many surprises, one of them being the ridiculously large amount of DNA that did not code for proteins – or anything at all. It seemed like the genome was just a huge chaotic mess sprinkled with tiny nuggets!

The reason this is misleading is because it totally misrepresents the history of the human genome. It's been four decades since we first became aware of the fact that only 1-2% of the human genome encoded proteins. This was hardly a surprise—in fact it was one of the principle arguments against sequencing the human genome. (What was the point of wasting all that money on DNA sequences that were mostly junk?)

One of the unfortunate characteristics of the junk DNA deniers is that they are completely unaware of the historical arguments in favor of junk DNA (e.g. False History and the Number of Genes, Genetic Load, Neutral Theory, and Junk DNA). Everyone who understood the problem was quite happy to find verification when the first draft of the human genome was published. It's exactly what the knowledgeable experts predicted.

The article raises the standard question that seems to have only recently occurred to some researchers; namely, what is all that DNA doing? It's mostly junk—at least that's the conclusion reached by many scientists back in the 1970s and most of what we've discovered since then has supported that view.

The development of new, cheap, sequencing technologies and the availability of an annotated standard human genome reference sequence has made it possible to look for new transposon insertions in a large number of individuals. The results can help confirm or refute the idea that most of our genome is junk.

A recently published article in PLoS Genetics describes the results of such an analysis (Stewart et al. 2011). It's part of the 1000 Genomes Project.

They detected a total of 7,310 insertions that were present in only a subset of the 179 genomes that were analyzed. About 85% of these were Alu elements, 12% were L1 LINES, and 3% were SVA's. This is consistent with earlier work that catalogued the number of active transposons in the human genome. As expected, very few of these insertions occurred in exons (39) and only 3 occurred in coding regions. This strongly suggests that there is strong selection against disruptions of coding regions. It implies that most of the detectable insertions occur in regions where disruption of the sequence has no effect on the viability of the the individual. In other words, insertions occur predominantly in junk DNA.

The authors examined the sequences of two families in order to assess the frequency of new transposon insertions. Earlier data indicated that a new insertion arises only once in every twenty births so it's not a surprise to find that the offspring in these two families showed no new insertions relative to their parents.

A data set of this size allows for an assessment of the rate of fixation of various new mobile element insertion (MEI) alleles in the population. The authors conclude,

MEI alleles propagate within population groups much like other predominantly neutral polymorphisms. MEI allele frequency spectra from the low coverage samples are in general agreement with expectations from the standard neutral model for allele drift in a population.

What this means is that most (perhaps all) of the insertion alleles are segregating as though they have no effect on the fitness of the individuals that carry them. This is further support for the idea that large parts of the genome are junk.

I recently learned a lot about steampunk by attending Polaris 25 last July. I'm thinking I should put together an outfit that I can wear around campus. I haven't seen a fashion statement that's as cool as steampunk since the 1960's.

John Hawks is obviously a fan as well. He's posted an article entitled Steampunk Genetics where he describes how predictions based on Victorian genetics are still more accurate than those based on genome sequences. The important point is that some heritable traits are still too complex to be attributed to specific alleles.

Thursday, September 15, 2011

The Discovery Institute is the leading proponent of Intelligent Design Creationism—a form of creationism that concentrates on proving evolution is wrong and therefore the history of life must be explained by the intervention of an intelligent designer (i.e. god).

The BioLogus Foundation was founded by Francis Collins and it brings together a group of theistic evolutionists. Theistic Evolution is a form of creationism that accepts much of evolutionary biology but still postulates the the history of life requires the intervention of a creator.

Friday, September 09, 2011

Up until now I have been proud of the fact that nobody is banned on Sandwalk. I delete all spam that consist entirely of threats and incoherent ranting (e.g. Dennis Markuze). I also delete spam that advertises products and/or commercial websites. But even the weirdest kooks are allowed to post comments as long as they don't post spam.

But there's one thing I won't tolerate and that's when people start threatening other bloggers and commenters by contacting their families or their employers. That's where I draw the line.

Doug Dobney has posted hundreds of comments on Sandwalk under "anonymous." He is apparently opposed to evolution and won't listen to reason from those who have tried to set him straight on the facts. That's fine with me. If others want to have fun with him here, then it's up to them. I've been ignoring him and so has almost everyone else.

Recently another commenter revealed that "anonymous" was, in fact, Doug Dobney, a well-known kook from Peterborough, Ontario, Canada. That made Doug very upset in spite of the fact that it was trivially easy to identify him based on his internet record where he has already admitted to his identity. (He also posts as "Socrates.")

That's fine too. What happened next is not fine. Doug Dobney sent letters to the Chair of my department and the Dean of the Faculty of Medicine complaining about me. Here's a copy of his letter.

Dear Dr. Whiteside:

I need to bring to your attention a serious problem that relates to the Department of Biochemistry.

Please see the emails below.

Not only has the problem not been addressed, but I have not even been given a response to my emails documenting this dangerous situation.

To give you some insight into this problem, here are three, of many, instances from Dr. Moran’s blog:

“Josef Gladstone said...

I don't even understand why Doug Dobney would even want to toil in anonytimity when he is doing such groundbreaking work on organism development, especially in the new field of pterosaur to bird development. He is truly one of the great minds of the 21st century.

Doug Dobney will eventually be viewed in the same light as Darwin by the time the history of organism development is written.

And of course, to quote the great Mr. Dobney, this is certainly not worth arguing about! (both his wonderful wife Angela and myself get a great chuckle out of this whenever he says it, which is quite often!)

“AND

Ddobney@moffathouse.ca said...

Hey Doug Dobney, do guests at the Moffat House know you're insane?

AND if your stomach is up to it, there is this link on the blog:

http://socratesisdougdobney.blogspot.com/

I would appreciate your attention to this serious problem.

Yours sincerely,

Douglas Dobney

That's something I will not tolerate. Doug Dobney has earned the distinction of being the very first person to be banned on Sandwalk

My Dean is a very busy person but I'm sure she enjoys a little chuckle now and then when these kook emails turn up in her mailbox. I'll have to ask her if she remembers Doug Dobney next time I see her in the line for coffee downstairs.

There are kooks everywhere. Some people believe they have been abducted by UFOs and others believe that the moon landings never happened. There are many who believe that the 9/11 tragedy was a conspiracy of the United states government.

One thing that all kooks have in common is their ability to completely detach themselves from reality. Wanna see a good example?

I hope the Discovery Institute has a full-time psychologist on their staff.

With the approaching 9/11 anniversary, Slate has been running a series tracing the rise and ongoing evolution of 9/11 Truth theories that try to show how the attacks 10 years ago were really an inside job. According to this thinking, 9/11 was no attack by Islamic terrorists. Rather, the towers were detonated by an expertly covered-up collusion among Zionists and U.S. government operatives. You might have expected these notions would, if entertained at all, be dispelled by the exhaustive debunking job that Popular Mechanics did with its 5,500-word article on the subject back in 2005. Not so, as those who take an interest in conspiracy culture know well.

What I found striking about the first installment in the Slate series, by Jeremy Stahl, is the parallels with what we know about the thought and writings of Evolution Truth activists: our ever-loving friends in the Darwin Lobby. You may recall the news of a few months back that Glenn Branch, deputy director of the Darwin-lobbying National Center for Science Education, had collaborated with 9/11 Truth conspiracist James H. Fetzer in editing a special number of the journal Synthese on "Evolution and Its Rivals." That issue of the journal became so notorious for the incivility of its contributions that a whole fracas broke out and made the pages of the New York Times.

It may have seemed just a delicious coincidence at the time to find Branch and Fetzer teaming up so comfortably. Yet consider the features of 9/11-style paranoid thinking and some similarities to its evolutionary counterpart ...

Coalition Calls for Defunding of Catholic Boards, End to Discrimination Against Gays in Publicly Funded Schools

KEEP THE FAITH—BUT NOT IN OUR SCHOOLS

The Canadian Secular Alliance and its allies are hosting a rally in front of the Legislature at Queen's Park on Sunday, September 18 from 1:30-3:30 p.m. to demand:

• The end of the over $500 million taxpayer subsidization for the promotion of the Roman Catholic religion. Public funding for the expensive duplicate school system must be eliminated to provide one secular publicly funded school system.

• The protection of equality rights for all students—including gay students—by ending the constitutional privilege afforded Roman Catholics to overrule legislation and the courts in favour of religious dogma.

"Equality for all students means ending privileged access to public schools for favoured religious services," says CSA President Greg Oliver.

Speakers represent a cross section of the religious and non-religious.

Wednesday, September 07, 2011

This month's Carnival of Evolution (39th version) is hosted by Cromercrox, a "Celebrity Nutritionist" who lives in Cromer, Norfolk, England (United Kingdom). It blogs at The End Of The Pier Show: Carnival of Evolution #39.

Thursday, September 01, 2011

We're in Brussels babysitting my granddaughter Zoë while her parents are house hunting in Los Angeles.

Yesterday we went to see the Canadian National Vimy Memorial on Vimy Ridge, the site of an important battle in April 1917. Thousands of Canadians died in the battle.

Zoë liked climbing on the steps and statues.

There are 11,000 names engraved on the memorial. They represent Canadian soldiers who died in France during World War I and whose remains were never recovered. One of the names is Lance Corporal Robert Alexander Hood (1895 - 1917), a distant cousin of Ms. Sandwalk. He died on April 12, in 1917 during the final days of the battle of Vimy Ridge.

Recent Comments

Principles of Biochemistry 5th edition

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

Superstition

Quotations

The old argument of design in nature, as given by Paley, which formerlyseemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.

Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.

The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.

Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.

The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.